A science company's disclosure that decisions on commercial fishing limits are essentially guesswork and "highly susceptible to influence" has led to an assurance from the New Zealand Fisheries Ministry that annual decisions on fish catch limits are based on "the best available science".

The ministry's deputy chief executive for fisheries management, Gavin Lockwood, says that every year NZD 20 million (USD 14 million) is spent on scientific research and stock assessments.

"We have sophisticated and well integrated fisheries research, management and monitoring systems that have been refined over the last 20 years," says Lockwood.

He spoke out after the National Institute of Water and Atmospheric Research (NIWA) chief fisheries scientist, John McKoy, told an online forum on the science behind fisheries management that the information used to set commercial catch limits needed to be improved.

But Lockwood says in a statement the quota management system (QMS) is regarded as one of the world's best, though the nation has to "carefully prioritise" spending on research that best meets fisheries management needs.

About 70 per cent of commercial catch comes from assessed fishstocks.

"The QMS gets a lot of international attention because it gives fisheries managers effective tools to maintain healthy fishstocks and rebuild depleted stocks when required, he says.

But McKoy says in the quota system, research targets the most valuable species as those that interested fishing companies, who pay for the research.

Less than a fifth of fish stocks managed under the QMS has enough information available to assess their status, and about a third of those are overfished, depleted or collapsed.

"For more than 80 per cent of our fish stocks, we have no idea about status and so setting catch levels is literally guesswork," she says in a statement.

The Fisheries Ministry only stepped in when stocks were fished down to 20 per cent of their original levels, says Knowles. Some stocks have been allowed to crash as low as 10 per cent of original levels before fishing was closed.

"If we don't learn more about the fish in our seas and the complex food webs, we risk the collapse of other fisheries like orange roughy," she says.

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